Hello, I need to test this tool : https://majiq.biociphers.org/
It asks to register by e-mail in order to see the installation page.
Basically the instructions say :
Before installation:
$ export HTSLIB_LIBRARY_DIR=/path/to/htslib/lib
$ export HTSLIB_INCLUDE_DIR=/path/to/htslib/include
#! Version of htslib > 1.10 required !
Installation:
$ python3 -m venv env
$ source env/bin/activate
$ pip install git+https://bitbucket.org/biociphers/majiq_academic.git
So I need to install a newer version of htslib :
curl -OL https://github.com/samtools/htslib/releases/download/1.13/htslib-1.13.tar.bz2
tar -xf htslib-1.13.tar.bz2
cd htslib-1.13
./configure --prefix=$HOME/Tools_Packages/htslib-1.13
...but ....
configure: error: ***libbzip2*** development files not found
The CRAM format may use bzip2 compression, which is implemented in HTSlib
by using compression routines from libbzip2 <http://www.bzip.org/>.
Building HTSlib requires libbzip2 development files to be installed on the
build machine; you may need to ensure a package such as libbz2-dev (on Debian
or Ubuntu Linux) or bzip2-devel (on RPM-based Linux distributions or Cygwin)
is installed.
But ,when I try :
wget http://vault.centos.org/7.9.2009/os/Source/SPackages/bzip2-1.0.6-13.el7.src.rpm
or :
yum install bzip2
I get following message:
There was a problem importing one of the Python modules
required to run yum. The error leading to this problem was:
/shared/ifbstor1/software/miniconda/envs/python-3.9/lib/liblzma.so.5: version `XZ_5.1.2alpha' not found (required by /lib64/librpmio.so.3)
Please install a package which provides this module, or
verify that the module is installed correctly.
It's possible that the above module doesn't match the
current version of Python, which is:
2.7.5 (default, Nov 16 2020, 22:23:17)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-44)]
A bit tired of all these dependencies and different versions requirements ! Don't know what to do anymore !
Could you verify if newer version of htslib & bzip can be installed Globally..
Or, if I should do it locally, how ? I am not familiar with "yum" installations.